feature/SOF-7509 optimize film nb

other/materials_designer/Introduction.ipynb

@@ -97,6 +97,8 @@
     "\n",
     "This notebook demonstrates a workflow for converting materials data from the [JARVIS](https://jarvis.nist.gov/) database into ESSE format for use with the Mat3ra.com platform.\n",
     "\n",
+    "#### [6.1.4. Optimize film position on interface](optimize_film_position.ipynb).\n",
+    "\n",
     "## 7. Read more\n",
     "\n",
     "### 7.1. Under the hood.\n",

other/materials_designer/optimize_film_position.ipynb

@@ -0,0 +1,288 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Optimize Interface Film Position\n",
+    "\n",
+    "Find most optimal position of the film on the substrate interface.\n",
+    "\n",
+    "<h2 style=\"color:green\">Usage</h2>\n",
+    "\n",
+    "1. Make sure to select Input Material from the list of available materials. Must be an interface.\n",
+    "1. Set notebook parameters in cell 1.2. below (or use the default values).\n",
+    "1. Click \"Run\" > \"Run All\" to run all cells.\n",
+    "1. Wait for the run to complete.\n",
+    "1. Scroll down to view results.\n",
+    "\n",
+    "## Notes\n",
+    "\n",
+    "- The optimization is performed on a 2D grid of x,y translations.\n",
+    "- Interface material must have atoms labeled \"0\" for the substrate and \"1\" for the film.\n",
+    "\n",
+    "\n",
+    "## 1. Prepare the Environment\n",
+    "### 1.1. Install Packages\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "4dc7b2ed495d66e0"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "\n",
+    "if sys.platform == \"emscripten\":\n",
+    "    import micropip\n",
+    "\n",
+    "    await micropip.install('mat3ra-api-examples', deps=False)\n",
+    "    from utils.jupyterlite import install_packages\n",
+    "\n",
+    "    await install_packages(\"\")\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "dd86bee2985f1b50",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 1.2. Set optimization parameters\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "cca70ab27ef1d01d"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "MATERIAL_INDEX = 0  # Index of the material to optimize\n",
+    "# Grid parameters\n",
+    "GRID_SIZE = (20, 20)  # Resolution of the x-y grid\n",
+    "GRID_RANGE_X = (-0.5, 0.5)  # Range to search in x direction\n",
+    "GRID_RANGE_Y = (-0.5, 0.5)  # Range to search in y direction\n",
+    "USE_CARTESIAN = False  # Whether to use Cartesian coordinates\n",
+    "\n",
+    "# Visualization parameters\n",
+    "SHOW_3D_LANDSCAPE = False  # Whether to show 3D energy landscape\n",
+    "STRUCTURE_REPETITIONS = [3, 3, 1]  # Repetitions for structure visualization\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "12878fd61f5a6b13",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 3. Load Material\n",
+    "### 3.1. Make sure that loaded material is an interface material (atoms must have labels \"0\" for the substrate and \"1\" for the film)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "463af646361cd982"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.jupyterlite import get_materials\n",
+    "\n",
+    "materials = get_materials(globals())\n",
+    "interface_material = materials[MATERIAL_INDEX]\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "3d982a1ca641f0d8"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 3.2. Visualize the Material\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "e920a6dd4906d8e8"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.visualize import visualize_materials\n",
+    "\n",
+    "visualize_materials([interface_material], repetitions=STRUCTURE_REPETITIONS)\n",
+    "visualize_materials([interface_material], repetitions=STRUCTURE_REPETITIONS, rotation='-90x')"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "5f4afdb7ac0c865b"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 3.3. Optimize Film Position"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "90255d774f62d1da"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.tools.build.interface import get_optimal_film_displacement\n",
+    "from mat3ra.made.tools.modify import interface_displace_part\n",
+    "from mat3ra.made.tools.calculate.calculators import InterfaceMaterialCalculator\n",
+    "from mat3ra.made.tools.optimize import evaluate_calculator_on_xy_grid\n",
+    "calculator = InterfaceMaterialCalculator()\n",
+    "\n",
+    "# Calculate energy landscape\n",
+    "xy_matrix, energy_matrix = evaluate_calculator_on_xy_grid(\n",
+    "    material=interface_material,\n",
+    "    calculator_function=calculator.get_energy,\n",
+    "    modifier=interface_displace_part,\n",
+    "    grid_size_xy=GRID_SIZE,\n",
+    "    grid_range_x=GRID_RANGE_X,\n",
+    "    grid_range_y=GRID_RANGE_Y,\n",
+    "    use_cartesian_coordinates=USE_CARTESIAN\n",
+    ")\n",
+    "\n",
+    "# Find optimal position\n",
+    "optimal_displacement = get_optimal_film_displacement(\n",
+    "    material=interface_material,\n",
+    "    calculator=calculator,\n",
+    "    grid_size_xy=GRID_SIZE,\n",
+    "    grid_range_x=GRID_RANGE_X,\n",
+    "    grid_range_y=GRID_RANGE_Y,\n",
+    "    use_cartesian_coordinates=USE_CARTESIAN\n",
+    ")\n",
+    "\n",
+    "print(f\"\\nOptimal displacement vector: {optimal_displacement}\")\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "eb0b6e59c24dda4"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 4. Visualize Results\n",
+    "### 4.1. Plot Energy Landscape"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "2945179d3729935d"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.plot import plot_energy_heatmap, plot_energy_landscape\n",
+    "# Plot energy landscape\n",
+    "plot_energy_heatmap(xy_matrix, energy_matrix, optimal_position=optimal_displacement[:2])\n",
+    "\n",
+    "if SHOW_3D_LANDSCAPE:\n",
+    "    plot_energy_landscape(xy_matrix, energy_matrix, optimal_position=optimal_displacement[:2])\n",
+    "\n",
+    "# Create optimized material\n",
+    "optimized_material = interface_displace_part(\n",
+    "    interface_material,\n",
+    "    displacement=optimal_displacement,\n",
+    "    use_cartesian_coordinates=USE_CARTESIAN\n",
+    ")\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "41ac6b383001db6b",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 4.1. Visualize Original and Optimized Materials"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "82a1af573c6ca0e9"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "print(\"\\nVisualization of original and optimized materials:\")\n",
+    "visualize_materials([interface_material, optimized_material],\n",
+    "                    repetitions=STRUCTURE_REPETITIONS)\n",
+    "visualize_materials([interface_material, optimized_material],\n",
+    "                    repetitions=STRUCTURE_REPETITIONS,\n",
+    "                    rotation='-90x')\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "e7972543ae747b68",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 5. Save Results\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "b4f6308e795e4f3c"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.jupyterlite import set_materials\n",
+    "\n",
+    "set_materials(optimized_material)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "c81ec652fbb64316",
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}